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comparison FalseDiscoveryRate.xml @ 4:6ead64a594bd draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
parents 3d84209d3178
children
comparison
equal deleted inserted replaced
3:ec62782f6c68 4:6ead64a594bd
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="FalseDiscoveryRate" name="FalseDiscoveryRate" version="1.12.0"> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
3 <description>Estimates the false discovery rate on peptide and protein level using decoy searches.</description> 3 <!--Proposed Tool Section: [ID Processing]-->
4 <macros> 4 <tool id="FalseDiscoveryRate" name="FalseDiscoveryRate" version="2.0.0">
5 <token name="@EXECUTABLE@">FalseDiscoveryRate</token> 5 <description>Estimates the false discovery rate on peptide and protein level using decoy searches.</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">FalseDiscoveryRate</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>FalseDiscoveryRate 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>FalseDiscoveryRate
11 14
12 -in ${param_in} 15 #if $param_in:
13 -fwd_in ${param_fwd_in} 16 -in $param_in
14 -rev_in ${param_rev_in} 17 #end if
15 -out ${param_out} 18 #if $param_in_target:
16 ${param_proteins_only} 19 -in_target $param_in_target
17 ${param_peptides_only} 20 #end if
18 -threads \${GALAXY_SLOTS:-24} 21 #if $param_in_decoy:
19 ${param_q_value} 22 -in_decoy $param_in_decoy
20 ${param_use_all_hits} 23 #end if
21 ${param_split_charge_variants} 24 #if $param_out:
22 ${param_treat_runs_separately} 25 -out $param_out
23 -algorithm:decoy_string ${param_decoy_string} 26 #end if
24 ${param_add_decoy_peptides} 27 #if $param_proteins_only:
28 -proteins_only
29 #end if
30 #if $param_peptides_only:
31 -peptides_only
32 #end if
33 -threads \${GALAXY_SLOTS:-24}
34 #if $param_algorithm_no_qvalues:
35 -algorithm:no_qvalues
36 #end if
37 #if $param_algorithm_use_all_hits:
38 -algorithm:use_all_hits
39 #end if
40 #if $param_algorithm_split_charge_variants:
41 -algorithm:split_charge_variants
42 #end if
43 #if $param_algorithm_treat_runs_separately:
44 -algorithm:treat_runs_separately
45 #end if
46 #if $param_algorithm_add_decoy_peptides:
47 -algorithm:add_decoy_peptides
48 #end if
49 #if $adv_opts.adv_opts_selector=='advanced':
50 #if $adv_opts.param_force:
51 -force
52 #end if
53 #end if
25 </command> 54 </command>
26 <inputs> 55 <inputs>
27 <param name="param_in" type="data" format="idXML" optional="True" label="Identification input file which contains a search against a concatenated sequence database. Either specify '-in' alone or 'fwd_in' together with 'rev_in' as input." help="(-in)"/> 56 <param format="xml" help="(-in) Either specify '-in' alone or 'in_target' together with 'in_decoy' as input" label="Identification input file containing a search against a concatenated sequence database" name="param_in" optional="True" type="data"/>
28 <param name="param_fwd_in" type="data" format="idXML" optional="True" label="Identification input to estimate FDR, forward run." help="(-fwd_in)"/> 57 <param format="xml" help="(-in_target) " label="Identification input file containing a search against a target-only database" name="param_in_target" optional="True" type="data"/>
29 <param name="param_rev_in" type="data" format="idXML" optional="True" label="Identification input to estimate FDR, decoy run." help="(-rev_in)"/> 58 <param format="xml" help="(-in_decoy) " label="Identification input file containing a search against a decoy-only database" name="param_in_decoy" optional="True" type="data"/>
30 <param name="param_proteins_only" type="boolean" truevalue="-proteins_only true" falsevalue="-proteins_only false" checked="false" optional="True" label="If set, the FDR of the proteins only is calculated" help="(-proteins_only)"/> 59 <param checked="false" falsevalue="" help="(-proteins_only) " label="If set only the FDR on protein level is calculated" name="param_proteins_only" optional="True" truevalue="-proteins_only" type="boolean"/>
31 <param name="param_peptides_only" type="boolean" truevalue="-peptides_only true" falsevalue="-peptides_only false" checked="false" optional="True" label="If set, the FDR of the peptides only is calculated" help="(-peptides_only)"/> 60 <param checked="false" falsevalue="" help="(-peptides_only) " label="If set only the FDR on peptide (PSM) level is calculated" name="param_peptides_only" optional="True" truevalue="-peptides_only" type="boolean"/>
32 <param name="param_q_value" type="boolean" truevalue="-algorithm:q_value true" falsevalue="-algorithm:q_value false" checked="true" optional="True" label="If 'true', the q-values will be calculated instead of the FDRs" help="(-q_value)"/> 61 <param checked="false" falsevalue="" help="(-no_qvalues) " label="If 'true' strict FDRs will be calculated instead of q-values (the default)" name="param_algorithm_no_qvalues" optional="True" truevalue="-algorithm:no_qvalues" type="boolean"/>
33 <param name="param_use_all_hits" type="boolean" truevalue="-algorithm:use_all_hits true" falsevalue="-algorithm:use_all_hits false" checked="false" optional="True" label="If 'true' not only the first hit, but all are used (peptides only)" help="(-use_all_hits)"/> 62 <param checked="false" falsevalue="" help="(-use_all_hits) " label="If 'true' not only the first hit, but all are used (peptides only)" name="param_algorithm_use_all_hits" optional="True" truevalue="-algorithm:use_all_hits" type="boolean"/>
34 <param name="param_split_charge_variants" type="boolean" truevalue="-algorithm:split_charge_variants true" falsevalue="-algorithm:split_charge_variants false" checked="false" optional="True" label="If set to 'true' charge variants are treated separately (for peptides of combined target/decoy searches only)." help="(-split_charge_variants)"/> 63 <param checked="false" falsevalue="" help="(-split_charge_variants) " label="If 'true' charge variants are treated separately (for peptides of combined target/decoy searches only)" name="param_algorithm_split_charge_variants" optional="True" truevalue="-algorithm:split_charge_variants" type="boolean"/>
35 <param name="param_treat_runs_separately" type="boolean" truevalue="-algorithm:treat_runs_separately true" falsevalue="-algorithm:treat_runs_separately false" checked="false" optional="True" label="If set to 'true' different search runs are treated separately (for peptides of combined target/decoy searches only)." help="(-treat_runs_separately)"/> 64 <param checked="false" falsevalue="" help="(-treat_runs_separately) " label="If 'true' different search runs are treated separately (for peptides of combined target/decoy searches only)" name="param_algorithm_treat_runs_separately" optional="True" truevalue="-algorithm:treat_runs_separately" type="boolean"/>
36 <param name="param_decoy_string" type="text" size="20" value="_rev" label="String which is appended at the accession of the protein to indicate that it is a decoy protein (for proteins only)." help="(-decoy_string)"/> 65 <param checked="false" falsevalue="" help="(-add_decoy_peptides) The q-value is set to the closest target score" label="If 'true' decoy peptides will be written to output file, too" name="param_algorithm_add_decoy_peptides" optional="True" truevalue="-algorithm:add_decoy_peptides" type="boolean"/>
37 <param name="param_add_decoy_peptides" type="boolean" truevalue="-algorithm:add_decoy_peptides true" falsevalue="-algorithm:add_decoy_peptides false" checked="false" optional="True" label="If set to true, decoy peptides will be written to output file, too. The q-value is set to the closest target score." help="(-add_decoy_peptides)"/> 66 <expand macro="advanced_options">
38 </inputs> 67 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
39 <outputs> 68 </expand>
40 <data name="param_out" label="Identification output with annotated FDR" format="idXML"/> 69 </inputs>
41 </outputs> 70 <outputs>
42 <help>**What it does** 71 <data format="xml" name="param_out"/>
43 72 </outputs>
44 Estimates the false discovery rate on peptide and protein level using decoy searches. 73 <help>Estimates the false discovery rate on peptide and protein level using decoy searches.
45 74
46 75
47 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FalseDiscoveryRate.html 76 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FalseDiscoveryRate.html</help>
48 77 </tool>
49 @REFERENCES@
50 </help>
51 </tool>